installing on a CentOS cluster without sudo rights

[genutis]

Hi, I've been having trouble getting seeker installed on my CentOS hpc. I looked at the previous thread from 2019, and it seemed to end with the author installing seeker using sudo privileges, and the user opting to install seekr on their local machine rather than their CentOS hpc, and the issue was closed.

Here is what I've tried:

$ conda create -n seekr python=3.8 $ conda activate seekr $ pip install seekr
Then the install errored out when it attempted to install louvain:

Building wheels for collected packages: louvain Building wheel for louvain (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-7gtp09kp cwd: /tmp/pip-install-b025btf_/louvain/ Complete output (4605 lines):
At then end of those 4605 lines I start to get some errors
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/pynterface.cpp: In function ‘PyObject* _set_rng_seed(PyObject*, PyObject*, PyObject*)’: src/pynterface.cpp:5:42: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"seed", NULL}; ^ gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/python_optimiser_interface.cpp -o build/temp.linux-x86_64-3.8/src/python_optimiser_interface.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_optimise_partition(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:43:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "partition", NULL}; ^ src/python_optimiser_interface.cpp:43:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_optimise_partition_multiplex(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:96:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nb_partitions != PyList_Size(py_layer_weights)) ^ src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_move_nodes(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "partition", "consider_comms", NULL}; ^ src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_set_consider_comms(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:220:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "consider_comms", NULL}; ^ src/python_optimiser_interface.cpp:220:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_get_consider_comms(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:251:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", NULL}; ^ src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_set_consider_empty_community(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:284:75: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "consider_empty_community", NULL}; ^ src/python_optimiser_interface.cpp:284:75: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_get_consider_empty_community(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:321:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", NULL}; ^ gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/python_partition_interface.cpp -o build/temp.linux-x86_64-3.8/src/python_partition_interface.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/python_partition_interface.cpp: In function ‘PyObject* _new_ModularityVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", NULL}; ^ src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_SignificanceVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:247:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", NULL}; ^ src/python_partition_interface.cpp:247:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_SurpriseVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", NULL}; ^ src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_CPMVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "node_sizes", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_RBERVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "node_sizes", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_RBConfigurationVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_get_py_igraph(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:608:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_from_coarse_partition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "membership", "coarse_node", NULL}; ^ src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_renumber_communities(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:755:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_diff_move(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "new_comm", NULL}; ^ src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_move_node(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "new_comm", NULL}; ^ src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_quality(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:859:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_aggregate_partition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:891:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_in_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:931:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:931:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_from_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:970:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:970:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_to_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1009:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:1009:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_in_all_comms(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1047:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_possible_edges_in_all_comms(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1079:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_weight_to_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "comm", NULL}; ^ src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_weight_from_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "comm", NULL}; ^ src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_get_membership(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1202:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_set_membership(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1245:61: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "membership", NULL}; ^ src/python_partition_interface.cpp:1245:61: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_get_resolution(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1303:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_set_resolution(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1332:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:1332:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_quality(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1366:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:1366:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] g++ -pthread -shared -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -L/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/lib -Wl,-rpath=/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/CPMVertexPartition.o build/temp.linux-x86_64-3.8/src/GraphHelper.o build/temp.linux-x86_64-3.8/src/LinearResolutionParameterVertexPartition.o build/temp.linux-x86_64-3.8/src/ModularityVertexPartition.o build/temp.linux-x86_64-3.8/src/MutableVertexPartition.o build/temp.linux-x86_64-3.8/src/Optimiser.o build/temp.linux-x86_64-3.8/src/RBConfigurationVertexPartition.o build/temp.linux-x86_64-3.8/src/RBERVertexPartition.o build/temp.linux-x86_64-3.8/src/ResolutionParameterVertexPartition.o build/temp.linux-x86_64-3.8/src/SignificanceVertexPartition.o build/temp.linux-x86_64-3.8/src/SurpriseVertexPartition.o build/temp.linux-x86_64-3.8/src/pynterface.o build/temp.linux-x86_64-3.8/src/python_optimiser_interface.o build/temp.linux-x86_64-3.8/src/python_partition_interface.o igraphcore/lib/libigraph.a /usr/lib64/libz.a /usr/lib64/libm.a -Ligraphcore/lib -L/usr/local/lib64 -L/usr/local/lib -L/usr/lib64 -L/usr/lib -L/lib64 -L/lib -lxml2 -lstdc++ -o build/lib.linux-x86_64-3.8/louvain/_c_louvain.cpython-38-x86_64-linux-gnu.so /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(branred.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(dosincos.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(sincos32.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin-fma4.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(sincos32-fma4.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(dosincos-fma4.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin-avx.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(k_standard.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_pow.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpatan.o): relocation R_X86_64_32S against symbol __atan_twonm1' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpsqrt.o): relocation R_X86_64_32S against symbol __mpsqrt_mp' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(slowpow.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_rint-c.o): relocation R_X86_64_32S against .rodata.cst16' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_pow-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(slowpow-fma4.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(halfulp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpatan-fma4.o): relocation R_X86_64_32S against symbol __atan_twonm1' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpsqrt-fma4.o): relocation R_X86_64_32S against symbol __mpsqrt_mp' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(halfulp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status error: command 'g++' failed with exit status 1
then after those errors I get this error:

ERROR: Failed building wheel for louvain Running setup.py clean for louvain Failed to build louvain Installing collected packages: texttable, python-igraph, louvain Running setup.py install for louvain ... error ERROR: Command errored out with exit status 1: command: /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-o4pvoxsj/install-record.txt --single-version-externally-managed --compile --install-headers /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8/louvain cwd: /tmp/pip-install-b025btf_/louvain/ Complete output (285 lines):

and in this block of 285 lines I get a lot of warnings

gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/CPMVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/CPMVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/GraphHelper.cpp -o build/temp.linux-x86_64-3.8/src/GraphHelper.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/LinearResolutionParameterVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/LinearResolutionParameterVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/ModularityVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/ModularityVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/MutableVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/MutableVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/Optimiser.cpp -o build/temp.linux-x86_64-3.8/src/Optimiser.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/Optimiser.cpp:493:12: warning: extra tokens at end of #endif directive [enabled by default] #endif DEBUG ^ src/Optimiser.cpp: In member function ‘double Optimiser::optimise_partition(std::vector<MutableVertexPartition*>, std::vector<double>)’: src/Optimiser.cpp:101:7: warning: variable ‘aggregate_further’ set but not used [-Wunused-but-set-variable] int aggregate_further = true; ^ src/Optimiser.cpp: In member function ‘double Optimiser::move_nodes(std::vector<MutableVertexPartition*>, std::vector<double>, int, int)’: src/Optimiser.cpp:327:14: warning: variable ‘graph’ set but not used [-Wunused-but-set-variable] Graph* graph = NULL; ^ gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/RBConfigurationVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/RBConfigurationVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/RBERVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/RBERVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/ResolutionParameterVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/ResolutionParameterVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/SignificanceVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/SignificanceVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/SurpriseVertexPartition.cpp -o build/temp.linux-x86_64-3.8/src/SurpriseVertexPartition.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/pynterface.cpp -o build/temp.linux-x86_64-3.8/src/pynterface.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/pynterface.cpp: In function ‘PyObject* _set_rng_seed(PyObject*, PyObject*, PyObject*)’: src/pynterface.cpp:5:42: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"seed", NULL}; ^ gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/python_optimiser_interface.cpp -o build/temp.linux-x86_64-3.8/src/python_optimiser_interface.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_optimise_partition(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:43:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "partition", NULL}; ^ src/python_optimiser_interface.cpp:43:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_optimise_partition_multiplex(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:96:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nb_partitions != PyList_Size(py_layer_weights)) ^ src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_move_nodes(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "partition", "consider_comms", NULL}; ^ src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp:170:78: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_set_consider_comms(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:220:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "consider_comms", NULL}; ^ src/python_optimiser_interface.cpp:220:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_get_consider_comms(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:251:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", NULL}; ^ src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_set_consider_empty_community(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:284:75: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", "consider_empty_community", NULL}; ^ src/python_optimiser_interface.cpp:284:75: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_optimiser_interface.cpp: In function ‘PyObject* _Optimiser_get_consider_empty_community(PyObject*, PyObject*, PyObject*)’: src/python_optimiser_interface.cpp:321:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"optimiser", NULL}; ^ gcc -pthread -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -Iigraphcore/include -I/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8 -c src/python_partition_interface.cpp -o build/temp.linux-x86_64-3.8/src/python_partition_interface.o cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] src/python_partition_interface.cpp: In function ‘PyObject* _new_ModularityVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", NULL}; ^ src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:176:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_SignificanceVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:247:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", NULL}; ^ src/python_partition_interface.cpp:247:65: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_SurpriseVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", NULL}; ^ src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:318:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_CPMVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "node_sizes", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:391:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_RBERVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "node_sizes", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:467:114: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _new_RBConfigurationVertexPartition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"graph", "initial_membership", "weights", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:539:100: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_get_py_igraph(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:608:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_from_coarse_partition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "membership", "coarse_node", NULL}; ^ src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:671:76: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_renumber_communities(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:755:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_diff_move(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "new_comm", NULL}; ^ src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:791:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_move_node(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "new_comm", NULL}; ^ src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:825:64: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_quality(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:859:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_aggregate_partition(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:891:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_in_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:931:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:931:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_from_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:970:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:970:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_to_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1009:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "comm", NULL}; ^ src/python_partition_interface.cpp:1009:55: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_weight_in_all_comms(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1047:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_total_possible_edges_in_all_comms(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1079:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_weight_to_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "comm", NULL}; ^ src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:1113:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_weight_from_comm(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "v", "comm", NULL}; ^ src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp:1159:60: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_get_membership(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1202:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _MutableVertexPartition_set_membership(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1245:61: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "membership", NULL}; ^ src/python_partition_interface.cpp:1245:61: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_get_resolution(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1303:47: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", NULL}; ^ src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_set_resolution(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1332:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:1332:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] src/python_partition_interface.cpp: In function ‘PyObject* _ResolutionParameterVertexPartition_quality(PyObject*, PyObject*, PyObject*)’: src/python_partition_interface.cpp:1366:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] static char* kwlist[] = {"partition", "resolution_parameter", NULL}; ^ src/python_partition_interface.cpp:1366:71: warning: deprecated conversion from string constant to ‘char*’ [-Wwrite-strings] g++ -pthread -shared -B /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat -L/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/lib -Wl,-rpath=/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.8/src/CPMVertexPartition.o build/temp.linux-x86_64-3.8/src/GraphHelper.o build/temp.linux-x86_64-3.8/src/LinearResolutionParameterVertexPartition.o build/temp.linux-x86_64-3.8/src/ModularityVertexPartition.o build/temp.linux-x86_64-3.8/src/MutableVertexPartition.o build/temp.linux-x86_64-3.8/src/Optimiser.o build/temp.linux-x86_64-3.8/src/RBConfigurationVertexPartition.o build/temp.linux-x86_64-3.8/src/RBERVertexPartition.o build/temp.linux-x86_64-3.8/src/ResolutionParameterVertexPartition.o build/temp.linux-x86_64-3.8/src/SignificanceVertexPartition.o build/temp.linux-x86_64-3.8/src/SurpriseVertexPartition.o build/temp.linux-x86_64-3.8/src/pynterface.o build/temp.linux-x86_64-3.8/src/python_optimiser_interface.o build/temp.linux-x86_64-3.8/src/python_partition_interface.o igraphcore/lib/libigraph.a /usr/lib64/libz.a /usr/lib64/libm.a -Ligraphcore/lib -L/usr/local/lib64 -L/usr/local/lib -L/usr/lib64 -L/usr/lib -L/lib64 -L/lib -lxml2 -lstdc++ -o build/lib.linux-x86_64-3.8/louvain/_c_louvain.cpython-38-x86_64-linux-gnu.so /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin.o): relocation R_X86_64_32S against symbol__sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(branred.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(dosincos.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(sincos32.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin-fma4.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(sincos32-fma4.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(dosincos-fma4.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_sin-avx.o): relocation R_X86_64_32S against symbol __sincostab' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(k_standard.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_pow.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpatan.o): relocation R_X86_64_32S against symbol __atan_twonm1' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpsqrt.o): relocation R_X86_64_32S against symbol __mpsqrt_mp' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(slowpow.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(s_rint-c.o): relocation R_X86_64_32S against .rodata.cst16' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_pow-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(slowpow-fma4.o): relocation R_X86_64_32 against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(halfulp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp-fma4.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpatan-fma4.o): relocation R_X86_64_32S against symbol __atan_twonm1' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpsqrt-fma4.o): relocation R_X86_64_32S against symbol __mpsqrt_mp' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_exp-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_log-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(e_atan2-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mplog-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpa-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp-avx.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(halfulp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC
/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: /usr/lib64/libm.a(mpexp.o): relocation R_X86_64_32S against .rodata' can not be used when making a shared object; recompile with -fPIC /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/compiler_compat/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status error: command 'g++' failed with exit status 1 ---------------------------------------- ERROR: Command errored out with exit status 1: /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/bin/python3.8 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"'; __file__='"'"'/tmp/pip-install-b025btf_/louvain/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-o4pvoxsj/install-record.txt --single-version-externally-managed --compile --install-headers /home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/include/python3.8/louvain Check the logs for full command output.

When running seekr in my seekr conda env at this point after this failed install, I also get this warning
-bash: /home/rcf-13/genutis/.local/bin/seekr: /home/cmb-07/sn1/genutis/software/anaconda2/envs/kmer/bin/python3.8: bad interpreter: No such file or directory

I used to have an anaconda2 install but have since purged everything, the anaconda2 folder in my software directory, any anaconda2 stuff in my $PATH, and any anaconda2 stuff in my .bash_profile or .bashrc, and have since moved to anaconda3, so I'm also scratching my head why seekr is looking for a file in an unrelated environment in an unrelated anaconda2 install that has since been deleted.

What could I try to do to get seekr installed? Thanks in advance!

[genutis]

I just tried cloning the repo and installing with setup.py, which introduces a different set of errors when seekr is run:

$ seekr Traceback (most recent call last): File "/home/rcf-13/genutis/.local/bin/seekr", line 6, in <module> from pkg_resources import load_entry_point File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3254, in <module> def _initialize_master_working_set(): File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3237, in _call_aside f(*args, **kwargs) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3266, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 584, in _build_master ws.require(__requires__) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 901, in require needed = self.resolve(parse_requirements(requirements)) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 787, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'python-igraph' distribution was not found and is required by seekr

so I tried to install python-igraph using pip, but its already installed:

$ pip3 install python-igraph --user WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. Requirement already satisfied: python-igraph in /auto/cmb-07/sn1/genutis/software/Python_packages/lib/python3.6/site-packages (0.8.0) Requirement already satisfied: texttable>=1.6.2 in /auto/cmb-07/sn1/genutis/software/Python_packages/lib/python3.6/site-packages (from python-igraph) (1.6.2)

then I tried installing python-igraph using conda:

$ conda install python-igraph

with the following installed:

`The following NEW packages will be INSTALLED:

cairo conda-forge/linux-64::cairo-1.16.0-hfb77d84_1002
fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001
freetype conda-forge/linux-64::freetype-2.10.0-he983fc9_1
gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
glib conda-forge/linux-64::glib-2.58.3-py38h6f030ca_1002
gmp conda-forge/linux-64::gmp-6.2.0-he1b5a44_2
icu conda-forge/linux-64::icu-64.2-he1b5a44_1
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1005
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_0
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002
libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0
pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0
pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
pycairo conda-forge/linux-64::pycairo-1.19.1-py38h438ddbb_0
python-igraph conda-forge/linux-64::python-igraph-0.8.0-py38h9e3b1fc_0
texttable conda-forge/noarch::texttable-1.6.2-py_0
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_`

but now louvain is giving me trouble again:

r$ seekr Traceback (most recent call last): File "/home/rcf-13/genutis/.local/bin/seekr", line 6, in <module> from pkg_resources import load_entry_point File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3254, in <module> def _initialize_master_working_set(): File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3237, in _call_aside f(*args, **kwargs) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3266, in _initialize_master_working_set working_set = WorkingSet._build_master() File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 584, in _build_master ws.require(__requires__) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 901, in require needed = self.resolve(parse_requirements(requirements)) File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr_source/lib/python3.8/site-packages/pkg_resources/__init__.py", line 787, in resolve raise DistributionNotFound(req, requirers) pkg_resources.DistributionNotFound: The 'louvain' distribution was not found and is required by seekr

so I try to install louvain using conda since that seemed to work with python igraph rather than pip:

conda install louvain

igraph conda-forge/linux-64::igraph-0.7.1-h9e3b1fc_1007 louvain conda-forge/linux-64::louvain-0.6.1-py38he1b5a44_2

and it seemed to have worked!!

$ seekr Welcome to SEEKR!

So to summarize, here are the commands that worked for me on my centos cluster:
conda create --name seekr_source python=3.8
conda activate seekr_source
git clone https://github.com/CalabreseLab/seekr.git
python3 setup.py install
conda install python-igraph
conda install louvain
seekr

[Jessime]

@genutis Nice! Thanks for figuring out what was going wrong. I've updated the README to include your install instruction.

https://github.com/CalabreseLab/seekr#centos

[Jessime]

@genutis Btw, you should pull the latest version of master. It looks like the newest networkx breaks things, so I've pinned the version for now to get tests passing again.

[genutis]

Hi Jessime! Thank you for the reply! I pulled the latest version and installed seekr in a fresh conda environment, but I get this error pertaining to networkx while working through the quickstart guide: $ seekr_graph example_vs_self.csv 0.13 -g example_vs_self.gml -c communities.csv Traceback (most recent call last): File "/home/cmb-07/sn1/genutis/software/anaconda3/envs/seekr/bin/seekr_graph", line 11, in <module> load_entry_point('seekr==1.4.2', 'console_scripts', 'seekr_graph')() File "/home/rcf-13/genutis/.local/lib/python3.8/site-packages/seekr/console_scripts.py", line 533, in console_graph _run_graph(args.adj, float(args.threshold), args.gml_path, args.csv_path, args.louvain, File "/home/rcf-13/genutis/.local/lib/python3.8/site-packages/seekr/console_scripts.py", line 509, in _run_graph maker.make_gml_csv_files() File "/home/rcf-13/genutis/.local/lib/python3.8/site-packages/seekr/graph.py", line 177, in make_gml_csv_files self.build() File "/home/rcf-13/genutis/.local/lib/python3.8/site-packages/seekr/graph.py", line 173, in build self.find_main_sub() File "/home/rcf-13/genutis/.local/lib/python3.8/site-packages/seekr/graph.py", line 93, in find_main_sub subgraphs = list(networkx.connected_component_subgraphs(self.graph)) AttributeError: module 'networkx' has no attribute ‘connected_component_subgraphs' I also tried to edit the setup.py file to require networkx 2.2 rather than 2.3, reinstalled seekr, and I got the same error. Thanks again for your work on this software! Best, Luke

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On Mar 6, 2020, at 10:01 AM, Jessime Kirk ***@***.***> wrote: @genutis Btw, you should pull the latest version of master. It looks like the newest networkx breaks things, so I've pinned the version for now to get tests passing again. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[Jessime]

That's super weird. Requiring 2.3 was an immediate fix for travis-ci. Are you sure python isn't being goofy and still installing 2.4 somehow? What happens if you do:

$ pip freeze | grep "networkx"

[genutis]

Hi Jessime, Thanks for the reply. Sure enough, networkx 2.4 is actually installed! I fixed my seekr conda environment using this command: $ pip install networkx==2.3 And now the quickstart guide is fully working. Thanks for the help and for being so responsive!! Best, Luke

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On Mar 9, 2020, at 3:22 PM, Jessime Kirk ***@***.***> wrote:  That's super weird. Requiring 2.3 was an immediate fix for travis-ci. Are you sure python isn't being goofy and still installing 2.4 somehow? What happens if you do: $ pip freeze | grep "networkx" — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[Jessime]

Python dependencies are the worst. 😢

Glad you got it working though, and feel free to open more issues if other things are broken!